Starting phenix.real_space_refine on Thu Nov 14 05:22:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jst_61782/11_2024/9jst_61782.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jst_61782/11_2024/9jst_61782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jst_61782/11_2024/9jst_61782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jst_61782/11_2024/9jst_61782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jst_61782/11_2024/9jst_61782.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9jst_61782/11_2024/9jst_61782.cif" } resolution = 1.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 8 5.16 5 C 1440 2.51 5 N 368 2.21 5 O 360 1.98 5 H 2128 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4304 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "B" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "E" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "F" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "G" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "H" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 538 Classifications: {'peptide': 35} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 33} Time building chain proxies: 2.63, per 1000 atoms: 0.61 Number of scatterers: 4304 At special positions: 0 Unit cell: (73.7856, 75.5424, 49.1904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 360 8.00 N 368 7.00 C 1440 6.00 H 2128 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 328.6 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 77.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 179 removed outlier: 6.866A pdb=" N LEU B 170 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER A 171 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE B 172 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 173 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 174 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 175 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 170 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER B 171 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 172 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY B 173 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 175 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 176 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 167 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU D 170 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY C 169 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N ILE D 172 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N SER C 171 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N THR D 174 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY C 173 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ARG D 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY C 175 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N MET D 178 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA C 177 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 164 removed outlier: 6.421A pdb=" N VAL G 150 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TRP H 153 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL G 152 " --> pdb=" O TRP H 153 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR H 155 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS G 154 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY H 157 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TRP G 156 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR H 159 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN G 158 " --> pdb=" O TYR H 159 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLN H 161 " --> pdb=" O GLN G 158 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP G 160 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU H 163 " --> pdb=" O TRP G 160 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 162 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 167 through 179 removed outlier: 6.402A pdb=" N VAL E 167 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU F 170 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY E 169 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N ILE F 172 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N SER E 171 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N THR F 174 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY E 173 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ARG F 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY E 175 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N MET F 178 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA E 177 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL F 167 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU G 170 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY F 169 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N ILE G 172 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N SER F 171 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N THR G 174 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY F 173 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ARG G 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY F 175 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N MET G 178 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA F 177 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU H 170 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER G 171 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE H 172 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY G 173 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR H 174 " --> pdb=" O GLY G 173 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 2128 1.12 - 1.29: 296 1.29 - 1.47: 967 1.47 - 1.64: 977 1.64 - 1.81: 16 Bond restraints: 4384 Sorted by residual: bond pdb=" CD1 TRP C 153 " pdb=" HD1 TRP C 153 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD1 TRP B 156 " pdb=" HD1 TRP B 156 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 TYR D 151 " pdb=" HD1 TYR D 151 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CZ2 TRP C 156 " pdb=" HZ2 TRP C 156 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CE1 TYR E 159 " pdb=" HE1 TYR E 159 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6045 1.90 - 3.81: 1311 3.81 - 5.71: 349 5.71 - 7.61: 122 7.61 - 9.52: 13 Bond angle restraints: 7840 Sorted by residual: angle pdb=" N GLY G 164 " pdb=" CA GLY G 164 " pdb=" C GLY G 164 " ideal model delta sigma weight residual 110.80 120.32 -9.52 1.41e+00 5.03e-01 4.56e+01 angle pdb=" N GLY F 164 " pdb=" CA GLY F 164 " pdb=" C GLY F 164 " ideal model delta sigma weight residual 110.80 120.13 -9.33 1.41e+00 5.03e-01 4.38e+01 angle pdb=" N GLY B 164 " pdb=" CA GLY B 164 " pdb=" C GLY B 164 " ideal model delta sigma weight residual 110.80 120.00 -9.20 1.41e+00 5.03e-01 4.26e+01 angle pdb=" N GLY C 164 " pdb=" CA GLY C 164 " pdb=" C GLY C 164 " ideal model delta sigma weight residual 110.80 119.69 -8.89 1.41e+00 5.03e-01 3.97e+01 angle pdb=" N GLY E 164 " pdb=" CA GLY E 164 " pdb=" C GLY E 164 " ideal model delta sigma weight residual 110.74 117.75 -7.01 1.37e+00 5.33e-01 2.62e+01 ... (remaining 7835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.08: 1750 13.08 - 26.16: 124 26.16 - 39.23: 23 39.23 - 52.31: 55 52.31 - 65.39: 88 Dihedral angle restraints: 2040 sinusoidal: 1032 harmonic: 1008 Sorted by residual: dihedral pdb=" CA LEU B 163 " pdb=" C LEU B 163 " pdb=" N GLY B 164 " pdb=" CA GLY B 164 " ideal model delta harmonic sigma weight residual -180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA LEU F 163 " pdb=" C LEU F 163 " pdb=" N GLY F 164 " pdb=" CA GLY F 164 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA TRP C 160 " pdb=" C TRP C 160 " pdb=" N GLN C 161 " pdb=" CA GLN C 161 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.061: 173 0.061 - 0.121: 118 0.121 - 0.180: 13 0.180 - 0.240: 0 0.240 - 0.299: 8 Chirality restraints: 312 Sorted by residual: chirality pdb=" CA SER G 148 " pdb=" N SER G 148 " pdb=" C SER G 148 " pdb=" CB SER G 148 " both_signs ideal model delta sigma weight residual False 2.57 2.27 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA SER C 148 " pdb=" N SER C 148 " pdb=" C SER C 148 " pdb=" CB SER C 148 " both_signs ideal model delta sigma weight residual False 2.57 2.28 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA SER H 148 " pdb=" N SER H 148 " pdb=" C SER H 148 " pdb=" CB SER H 148 " both_signs ideal model delta sigma weight residual False 2.57 2.28 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 309 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 160 " 0.048 2.00e-02 2.50e+03 3.95e-02 6.25e+01 pdb=" CG TRP G 160 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP G 160 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP G 160 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP G 160 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP G 160 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP G 160 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 160 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 160 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP G 160 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP G 160 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TRP G 160 " -0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP G 160 " -0.034 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 160 " 0.056 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 160 " -0.044 2.00e-02 2.50e+03 pdb=" HH2 TRP G 160 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 153 " 0.089 2.00e-02 2.50e+03 3.86e-02 5.96e+01 pdb=" CG TRP D 153 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 153 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP D 153 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 153 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP D 153 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP D 153 " -0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 153 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 153 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP D 153 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TRP D 153 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TRP D 153 " -0.070 2.00e-02 2.50e+03 pdb=" HE3 TRP D 153 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 153 " 0.048 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 153 " -0.040 2.00e-02 2.50e+03 pdb=" HH2 TRP D 153 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " -0.032 2.00e-02 2.50e+03 3.58e-02 5.12e+01 pdb=" CG TRP B 160 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP B 160 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 160 " 0.102 2.00e-02 2.50e+03 pdb=" HE3 TRP B 160 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 160 " -0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 160 " 0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP B 160 " -0.010 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 751 2.36 - 2.92: 8880 2.92 - 3.48: 11156 3.48 - 4.04: 15822 4.04 - 4.60: 20968 Nonbonded interactions: 57577 Sorted by model distance: nonbonded pdb=" O VAL G 162 " pdb=" H LEU H 163 " model vdw 1.795 2.450 nonbonded pdb="HE21 GLN F 161 " pdb=" OE1 GLN G 161 " model vdw 1.814 2.450 nonbonded pdb=" H VAL G 162 " pdb=" O GLN H 161 " model vdw 1.816 2.450 nonbonded pdb="HE21 GLN B 161 " pdb=" OE1 GLN C 161 " model vdw 1.817 2.450 nonbonded pdb="HE21 GLN A 161 " pdb=" OE1 GLN B 161 " model vdw 1.817 2.450 ... (remaining 57572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.037 2256 Z= 0.828 Angle : 1.743 9.519 3072 Z= 1.159 Chirality : 0.080 0.299 312 Planarity : 0.010 0.038 360 Dihedral : 10.675 48.282 712 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.92 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.013 TRP D 153 HIS 0.007 0.002 HIS G 182 PHE 0.014 0.004 PHE G 149 TYR 0.066 0.013 TYR E 151 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 3.0731 time to fit residues: 134.5183 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2256 Z= 0.195 Angle : 0.615 4.027 3072 Z= 0.337 Chirality : 0.051 0.124 312 Planarity : 0.005 0.041 360 Dihedral : 7.182 23.731 296 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.46 % Allowed : 7.41 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 153 HIS 0.002 0.001 HIS E 182 PHE 0.003 0.001 PHE A 149 TYR 0.007 0.001 TYR B 159 ARG 0.002 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 3.4154 time to fit residues: 142.1495 Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2256 Z= 0.179 Angle : 0.589 4.180 3072 Z= 0.318 Chirality : 0.051 0.130 312 Planarity : 0.004 0.037 360 Dihedral : 7.171 25.169 296 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 5.56 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.44), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.005 0.001 PHE C 149 TYR 0.006 0.001 TYR H 159 ARG 0.001 0.000 ARG G 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 3.4713 time to fit residues: 144.5214 Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2256 Z= 0.185 Angle : 0.585 4.369 3072 Z= 0.315 Chirality : 0.051 0.128 312 Planarity : 0.004 0.034 360 Dihedral : 7.151 25.944 296 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.85 % Allowed : 5.09 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.45), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 153 HIS 0.001 0.000 HIS G 182 PHE 0.005 0.001 PHE C 149 TYR 0.005 0.001 TYR H 159 ARG 0.001 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.347 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 2.9881 time to fit residues: 112.1929 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2256 Z= 0.153 Angle : 0.558 4.497 3072 Z= 0.294 Chirality : 0.051 0.126 312 Planarity : 0.003 0.031 360 Dihedral : 6.788 23.289 296 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.85 % Allowed : 5.56 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 153 HIS 0.000 0.000 HIS G 182 PHE 0.004 0.001 PHE C 149 TYR 0.004 0.001 TYR C 151 ARG 0.002 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.360 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7880 time to fit residues: 142.1587 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2256 Z= 0.195 Angle : 0.610 5.395 3072 Z= 0.320 Chirality : 0.051 0.127 312 Planarity : 0.004 0.033 360 Dihedral : 7.112 26.339 296 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 6.48 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 153 HIS 0.001 0.000 HIS E 182 PHE 0.006 0.001 PHE C 149 TYR 0.005 0.001 TYR H 159 ARG 0.001 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.280 Fit side-chains REVERT: E 176 ARG cc_start: 0.7488 (ttm170) cc_final: 0.7220 (ttm170) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7628 time to fit residues: 141.2286 Evaluate side-chains 39 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 0.1980 chunk 2 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2256 Z= 0.177 Angle : 0.589 5.030 3072 Z= 0.309 Chirality : 0.051 0.128 312 Planarity : 0.004 0.034 360 Dihedral : 6.966 25.676 296 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.85 % Allowed : 6.48 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 153 HIS 0.001 0.000 HIS G 182 PHE 0.005 0.001 PHE C 149 TYR 0.004 0.001 TYR H 159 ARG 0.001 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.381 Fit side-chains REVERT: E 176 ARG cc_start: 0.7478 (ttm170) cc_final: 0.7216 (ttm170) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.8753 time to fit residues: 145.5422 Evaluate side-chains 38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2256 Z= 0.154 Angle : 0.561 4.790 3072 Z= 0.292 Chirality : 0.051 0.126 312 Planarity : 0.003 0.030 360 Dihedral : 6.627 22.831 296 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 7.41 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 153 HIS 0.001 0.000 HIS G 182 PHE 0.004 0.001 PHE C 149 TYR 0.004 0.001 TYR B 159 ARG 0.001 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.373 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7878 time to fit residues: 142.2270 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2256 Z= 0.143 Angle : 0.543 4.728 3072 Z= 0.281 Chirality : 0.051 0.125 312 Planarity : 0.003 0.027 360 Dihedral : 6.381 20.826 296 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.85 % Allowed : 6.48 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 153 HIS 0.000 0.000 HIS G 182 PHE 0.004 0.001 PHE C 149 TYR 0.004 0.001 TYR F 159 ARG 0.000 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.325 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.6953 time to fit residues: 138.6605 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2256 Z= 0.150 Angle : 0.556 4.764 3072 Z= 0.288 Chirality : 0.051 0.125 312 Planarity : 0.003 0.028 360 Dihedral : 6.467 22.128 296 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 7.41 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 153 HIS 0.000 0.000 HIS G 182 PHE 0.004 0.001 PHE C 149 TYR 0.004 0.001 TYR H 159 ARG 0.001 0.000 ARG C 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.356 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 3.7462 time to fit residues: 140.6180 Evaluate side-chains 37 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.154872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111905 restraints weight = 3871.161| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.36 r_work: 0.3303 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3087 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9313 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2256 Z= 0.210 Angle : 0.614 5.319 3072 Z= 0.323 Chirality : 0.052 0.127 312 Planarity : 0.004 0.033 360 Dihedral : 7.063 26.605 296 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.85 % Allowed : 7.87 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 153 HIS 0.001 0.000 HIS A 182 PHE 0.007 0.001 PHE C 149 TYR 0.005 0.001 TYR H 159 ARG 0.001 0.000 ARG G 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.08 seconds wall clock time: 59 minutes 48.96 seconds (3588.96 seconds total)